Isolation
by A Kiss Before Dying
Summary: What happens when that which was once bits and pieces of computer data and memory... turns human? Dedicated to the awesomeness that is Cortana. Set during the first Halo. HIATUS - SEE PROFILE
1. Chapter One

**DISCLAIMER: **I claim no ownership over any characters or situations taken from the Halo games and/or books.

My first Halo fic, despite the fact that I've been playing the games for years. I want to know how this story turns out with the readers in the Halo community before I continue much farther, so reviews are welcome, as well as constructive criticism. Thanks, and enjoy!

* * *

**CHAPTER 1**

"Touch down in five, Helljumpers! Prepare for possible enemy contact!" the gruff voice of the Pelican's pilot otherwise known as Melissa McKay echoed over twelve radio headsets. The men and women aboard the small bird responded to their captain's announcement with drawn weapons, resounding _clicks _of magazine changes, and eager faces, all of them ready for battle.

Their objective: infiltrate the map room; recover the Silent Cartographer. Eliminate any alien resistance.

The Orbital Drop Shock Troopers, or ODSTs, more aptly known as Helljumpers, had been the first group to leave the _Pillar of Autumn._ Recovering from the initial shock of losing their mother ship and becoming marooned on the strange new ring planet, Halo, the scattered Marines quickly grouped back together, taking over a small, alien-infested butte now renamed Alpha Base.

Met there by Captain Jacob Keyes and another group of recovered Marines from the _Autumn_,the Lieutenant, upon learning the terrible secrets Halo harvested at its core, instantly dispatched the Helljumpers once more to find an underground map room known only as the Silent Cartographer.

And so they were now; only, Keyes had also sent a second surprise with them, one the Helljumpers were most glad to see.

Amongst the ODSTs boarded up in the Pelican's troop bay stood the Master Chief; last remaining Spartan from the operation on Reach, protocol number 117.

His olive green armor, though slightly rusted and burned in places from the effects of battle, still glinted slightly from the overhead lights; his yellow visor shielded his face, but inside the HUD was a different story. Images constantly flashed across the makeshift 'screen'; in one corner, his shield status displayed as a small bar; in another, the ammo count in his M6D pistol and battle rifle.

Suddenly, the Chief heard a fairly new but seemingly familiar voice.

"How you holding up, Chief?" The playful, yet slightly concerned voice of the _Autumn's_ AI, Cortana, echoed from the back of his helmet.

Small and petite, the young AI named Cortana had one hand wrapped around a slim waist, the other idly twirling around a strand of short, cropped hair; or, at least that's how the Chief pictured her. Digital numbers, codes, and other analyzed data constantly scrolled across her body, emitting and giving her a blue, purple, and sometimes pink, hue.

"Swell, thanks," the Chief responded roughly; his voice was monotone and gravelly, stoic enough to give off an almost robotic impression, but the Chief was far from such, and no Marine could say so without witnessing the Spartan in battle—thus the reason they were glad to have him aboard.

Plasma fire from a nearby Jackal's pistol suddenly rocked the Pelican, causing its shields to flare. Curses flew as the Helljumpers grabbed onto leather straps hanging above their heads to keep their footing; Master Chief braced his hands and feet wide, gripping the sides of the hold to steady himself.

"Report!" McKay's voice shouted through the group intercom as soon as she regained control of the bird, "What in the Hell is down there?"

One of the Marines grasped the edges of the transport, leaning out the open cockpit at the back of the drop ship to examine the terrain below; the Pelican cruised low over a small beach, infested with all sorts of aliens: Elites, Grunts, and Jackals alike.

"Bad news, ma'am," the Marine reported back over his headset, "the landing area is crawling with the bastards."

"Damn," McKay spat, slamming a hand down on the dashboard; frustrated with the setback but not deterred, she brought the Pelican around in a slow circle around the beach, her eyes scanning for the safest landing area.

Finally spotting out a small peninsula of land not far from the war zone, McKay brought the Pelican down slowly, opening the back hatch where her troops were waiting further to allow them easy leaping access out of the transport.

"Helljumpers!" McKay barked over the intercom one last time before she dispatched her troops onto the bizarre planet's surface; unsure if she would ever see them again, the young Marine wanted to practice their time-honored ritual one last time. "How will you leave?"

"WE GO FEET FIRST!" The ODSTs roared in unison.

McKay smiled grimly. "Damned right you do."

With a sigh of resignation, she brought the Pelican to a hover directly over the beach. "LZ's hot, boys. Let the Chief go first," McKay ordered. "Follow his lead. Good luck, Marines; bring me back that map."

A scattered rally of "aye aye, ma'am," came up from the ODSTs as they all gathered around the opened hatch, preparing themselves for the jump and the skirmish that awaited them on the beach below.

The Chief stood in front of the small group of Marines, ready to lead them into the battle head on, when Cortana unexpectedly turned on her frequency to the twelve other men and women standing behind them.

"Give 'em hell, Marines," she stated boldly, her face alight with excitement.

Behind his shielded visor, Master Chief grinned at the AI's infamous announcement; and, with the newfound courage she had given them, the Chief leaped out of the Pelican's hold.

The Helljumpers were instantly met by a barrage of plasma fire. Several Marines fell instantly at the onslaught, but the rest sought cover behind scattered rocks, boulders, and the overhanging cliffs; the true reason McKay had set them down in that precise spot.

As soon as the Marines were able to return fire, the aliens began to fall. Squeals and barks echoed around the canyon as Grunts and Jackals—preferred war fodder by the higher ranking Elites—soon scattered the beach and shallow waters, the bright blue from the Grunts' methane tanks staining the sand and rocks.

Diving for cover behind the nearest boulder, Master Chief kept his back against the rock and scanned the immediate area for the closest break in the aliens' ranks. Spotting a clearing in the plasma fire, the Chief spun out from behind the rocks and shot several sustained bursts with his battle rifle.

A Jackal and two Grunts fell instantly. Cutting his way through the enemy's front line, the Chief fell several more of the Covenant forces, clearing a path for the Helljumpers to follow. They let up cries of triumph as they brought down their share of the aliens in the process.

Making their way gradually across the infested beach, the ODSTs and Master Chief had cleared most of the area of enemy resistance, when a second wave of Grunts and Elites raced down the mountain side to their left. Plasma bullets rained down on the flanked Marines, and several more dropped dead. The rest returned fire, scattering once more across the body-strewn beach.

As he ran for cover, a plasma grenade—thrown by a flanking Elite—suddenly stuck itself at the sand at the Chief's feet. The pulsing blue orb hummed loudly, ready to detonate within the second. Master Chief sprung backwards, but not quick enough; the grenade exploded, propelling him further along in his leap, finally landing him roughly on the ground several yards away.

Shaking his head to recover his senses, Master Chief stood up slowly, his vision fuzzy and blurred. Leveling his pistol, he went to take aim at the nearest Grunt and found his aim horribly off; he could not focus.

"Shake it off, Chief," Cortana told him urgently, "are you alright?"

Slowly recovering from the plasma grenade's blow, Master Chief wavered slightly on his feet, as he gradually came to his senses. Unfortunately, not even the cybernetic enhancements of a Spartan could allow him to recover fast enough to notice the red armor-clad Elite approaching him from behind.

Pain suddenly ripped through his skull as the butt of the alien's plasma rifle suddenly struck Master Chief in the head. He dropped to his knees in pain, struggling to grip consciousness. As he fell, the sheer force of the Elite's blow rocked his helmet from his head; slumping face first into the sand, the helmet rolled off his shoulders to land several inches in front of him.

The Elite cocked its head to one side curiously; the Demon's tool could possibly prove to be beneficial. He reached out with one clawed hand and grabbed it.

"Chief!" Cortana's voice cried out desperately from the HUD as the Elite dragged the helmet across the sand. It brought the helmet up to its angular face, studying it curiously before slinging it over its shoulder. "Chief! Over here!"

Only the echoes of her own voice answered her; suddenly, with a jolt of horrible realization, Cortana realized that the only frequency she was connected to was her own.

And so, mankind's worst fear had just came true; the enemy had Cortana. Had their data, stats, ship and body counts, valuable war information.

Had Earth.

* * *

A red-clad Elite by the name of R'izaymmir stalked down the long, dimly lit hallway of the Covenant warship, _Truth and Reconciliation_. He had just received word of his troops' skirmish down on the beach, and was on his way to the dungeons to examine the newest prisoners.

Throwing open the doors, R'izaymmir's mere presence caused the other Elites on guard to snap to attention; R'izaymmir nodded them at ease before slowly beginning to pace in front of the cells, examining the captives that lay inside.

Several petrified Privates cowered in the corners of their prison as R'izaymmir's shadow passed over them, yet they had nothing to fear, for the Elite had passed them by. R'izaymmir had seen his share of the human scum already, and clicked his split mandibles in disappointment. He had hoped for a different group of hostages this time.

As he neared the last cell, his wish came true. Peering in curiously through the bars, R'izaymmir noticed the last detainee resembled nothing of the Marines he had seen on a regular basis.

Lying towards the back of the cell, knees drawn up to her chin and seemingly asleep, was a young human woman.

The alien's dark, slanted eyes opened wide in surprise. Whirling around, R'izaymmir demanded in a rough, monotone bark, "where did this prisoner come from?"

One of the blue Elites standing guard stepped forward, the same Elite who had snatched up the Master Chief's helmet during the skirmish.

"Sir," he began apprehensively, clearly uncomfortable with the situation at hand, "the Demon appeared during our fight with the human scum…he was knocked down by a plasma grenade, and his helmet fell loose. I snatched it up; I thought it might prove useful to us. When we brought it back to the _Reconciliation _to be analyzed, a hologram of the human female appeared…and then she," he motioned to the cell to signal the young woman, "materialized. Sir…" he began again, more eagerly, "we think it was the humans' ship's AI."

"AI?" R'izaymmir breathed in disbelief, turning back around slowly to gaze down at the imprisoned girl in the cell. His split jaw quivered excitedly and, if it was at all possible for the alien, showed the beginnings of a grin.

"She could prove quite useful."

* * *

The floor of the dungeon they had put her in was cold.

Cortana unconsciously ran a fingertip between the cracks of concrete on the ground. Her whole body shivered, and her eyes were squeezed shut, as if to ward off the whole nightmare she was suddenly thrust into.

The floor was very cold indeed…how she wished she had a blanket to bring back the warmth…

Cortana's eyes suddenly flew open in alarm.

Since when could she feel?

Slowly lifting her head off the ground, Cortana's eyes darted around the small prison, searching for some explanation. It was all just a dream…it had to be. During the battle, the Chief was knocked unconscious, and—

A stray hand suddenly made its way through the short locks of Cortana's hair. She felt the strands run through her stray fingertips.

Startled, she ripped her hand away and held it in front of her face. Her skin was no longer blue, holographic, and streaming with data— her hands were real. Touchable. Human.

How was this possible? The AI's mind reeled with sudden incomprehension, a feeling she was not accustomed to.

Cortana quickly examined the rest of her body, as if to reassure herself that it was all real. Much to her bewilderment, it was; and, much to her embarrassment, she suddenly realized that she was naked. The other captured Marines all had their eyes trained on her, more out of curiosity than anything else.

Hastily sitting upright, Cortana drew her knees up tight against her new body. She glowered at the other Marines, motioning her hand around in the air wildly for them to turn away. Most of them did, but she was still cold, and a lone Private in the cell next to her handed a small blanket through the bars.

Sighing with relief, Cortana grinned and took the blanket gratefully from the Marine. She opened her mouth to thank him, but only a feral gurgle escaped her throat.

Cortana's fingers flew to her lips in surprise; she opened her mouth again to speak, brows furrowed in frustration, but only the same, feeble noise escaped from her lips.

Her face fell; she could not speak. The kind young man who had offered the AI his blanket suddenly drew back into his cell, startled and afraid.

As she wrapped the flimsy blanket tight around her shoulders; pulling back into the shadows, away from the puzzled stares of her other inmates, Cortana felt more cold and alone than she ever had before. The feeling was new for the AI, and Cortana silently wondered why humans had been cursed with emotions that could hurt.

The other POWs had stopped gawking at her through the bars of their own prison; Cortana suspected these men were too broken to care. Women were not uncommon in the war—Marines like Melissa McKay were a fierce example of that—but if she couldn't tell them who she was, how could she expect to survive a war… when she had no idea how to be human?


	2. Chapter Two

**AUTHOR'S NOTE:** Two and a half years is a long time to wait for an update… I'd like to thank everyone for the generous reviews and for having a seemingly endless amount of patience with me when it comes to this story. I didn't know this story would be received half as well as it was, and I can't apologize enough for not updating sooner. I hope this chapter makes up for the fact that I put off working on this story for far too long. Thanks to everyone for their support.

* * *

**CHAPTER 2**

As Master Chief lay in the sand on the beach, his mind reeled with the events of the past few minutes.

His brain was still hazy, his judgment clouded, no thanks to a lucky toss of a plasma grenade that had caught his armor and detonated, sending him flying across the beach. No sooner than he struggled to recollect himself, however, than he heard someone call his name.

"Chief!" The Spartan glanced up as a young Marine jogged up to him.

"Are you alright? That was some battle, huh? But we chased the alien bastards off! On your call, we can..."

The private trailed off as he drew closer, stopping several feet away. Master Chief staggered to his feet, gripping the sides of his head. His dark blonde hair was lank and matted in places, and one side of his cheek was singed from the plasma grenade blast that took off his helmet.

"God…" the Marine whispered, taking a hesitant step back. Chief realized his physical appearance must be shocking; years of masquerading behind stale green armor made others view him as more Spartan than human.

"S…sir, your helmet…" The Marine's voice shook as he hesitantly reached down and plucked the Chief's helmet from where it lay in the sand. One whole side was blackened from the burn of the plasma grenade, and Chief took it from the solider with a nod of thanks. He quickly placed it back on his head.

"Cortana." Chief spoke into his HUD in a commanding tone, prepared to get his plans back on track and take the scattered group of Marines inside the Covenant stronghold to retrieve the Silent Cartographer.

When she didn't automatically reply, he spoke again. "Cortana, do you read me?"

Still no answer. Chief grew apprehensive; since when had Cortana ever ignored him? He reached a hand behind his head, feeling for the slot in his helmet where the AI's memory chip fit into his HUD.

His blood ran cold when he realized it was no longer there.

"Sir?"

Chief glanced up, noticing the scared Marine still stood in front of him, as if awaiting orders. "Master Chief, sir, the mission…" he repeated, motioning halfheartedly over his shoulder, where the Covenant stronghold cast daunting shadows over the war-ridden beach.

Chief realized he had a decision to make. Continue on with the mission—turning back now would surely get him dishonorably discharged from the ranks of the UNSC—or return to his base and commander to report that Cortana, the army's most valued AI, was missing, possibly stolen by the dreaded Covenant forces.

His eyes sweeping over the beach once more, Master Chief's gaze fell on the remaining Marines scattered along the shoreline, struggling to recover in the aftermath of their unexpected battle with Covenant forces.

Chief turned back to the nervous young Marine standing in front of him, his next words carrying the weight of a difficult decision.

"Take me to Sergeant Johnson."

* * *

Cortana realized that in order to appreciate being the computerized AI of a massive war ship—compared to actually being on board one, in the flesh and bone—she had to walk a mile in the shoes of a human, as the saying went.

Provided she had some, of course.

Being a prisoner of war had less of a shock on her than abruptly and unexpectedly turning human did. However, gazing out into the world through the eyes of a Spartan didn't mean she was familiar with being one. Her body, her actions, even her voice had always acted in accordance with the ship, John-117, or what Johnson had programmed her to do. Now that she was inexplicably human, however, she had to learn how to do everything all over again.

Cortana sat contemplating all of this in a small, dank cell aboard the Covenant ship, huddled in one corner with her knees pulled up to her chin. She had since been given a thinning, dirtied wrap to cover her body, and nothing else.

The Covenant forces keeping her and other Marines prisoner occasionally passed stale bread and water through the bars, providing them with enough nutrition to keep them alive. One blue-clad Elite did so now, sliding rations to each of the prisoners and snapping with split mandibles at anyone who got too close to the bars.

Cortana reached for the plate and cup of water as it was passed to her, pulling the rations closer with slightly trembling hands. Even simple actions such as picking up the bread and cup to nourish her body had become a chore; never having the need to touch such material items before made it all the more difficult to learn how to do so now.

The other Marines had since ceased attempting to communicate with her. Cortana frowned as the other men apprehensively watched her fumbling with her rations through the bars of their own prison. They had asked her what her name was, what team she had been with, what ship she came down on; all of these questions she had been unable to answer, because she had yet to learn how to make her human body speak.

She sighed, wrapping thin fingers around her neck, frustrated with having to learn all the basic human skills at a child's pace. How long would it be before she could act on her own accord again, and set things right?

For the first time in what seemed like ages, Cortana wished John was there with her. She was always the one to give him advice; now she found herself seeking his. Why had she gone from shipmate and AI to living in flesh and blood? Why couldn't have any sort of control over her own body?

Cortana turned the seemingly endless amount of questions over and over again in her mind as she sat hunched over in one corner of her prison, consuming the stale bread with all the grace of a two-year-old. Despite her newfound, human-like qualities of modesty, she had always been used to being intelligent—she was the AI for the _Pillar of Autumn­, _after all—but to not be able to answer her own questions was unbearably frustrating.

For how to you explain turning bits and pieces of data and memory into a human being?

* * *

Several hours later, a pair of blue-clad Elites, accompanied by their higher-ranking commander, R'izaymmir, entered the holding cell of the Covenant ship. As it is with any alien species, the Covenant wished to analyze and examine their captives in order to better understand the enemy they were fighting against… and to gain any useful military information in the process.

Their methods of torture, however, were not so alien to the prisoners as their captives were.

"Out, maggots," R'izaymmir snarled, shoving the Marines forcefully from the cells and into line. The other two Elites prowled up and down the growing length of the newly acquired prisoners as their red-clad officer collected the rest.

Cortana's cell was the last in a long line of holding areas. R'izaymmir approached, jerking the barred door open with a quick turn of the key as he reached in and pulled Cortana out and into line with the other.

She did not protest as she was roughly removed from her cell; as far as she was concerned, the less trouble she caused with her captors, the more likely she was to make it away from them alive.

As she stood in line behind the rest of her fellow captured Marines, waiting to be escorted to whatever hellish area of the Covenant ship awaited her next, Cortana winced as a dull ache began to pulse in her head.

The pain grew steadily worse, climbing to a screeching crescendo that caused Cortana to clap her hands around the sides of her temples, silently screaming in pain. The high-pitched frequencies and whines shot through her brain like a bullet, leaving a throbbing sense agony it its wake; Cortana dropped to her knees, hands clutching at her short brown hair, trying to rid her mind of the pain.

Images began to dance behind her eyelids then, long-forgotten symbols of a dead race, architectural designs and laid-out plans for buildings and other objects that resembled Halo and other Forerunner artifacts, and data even the former AI couldn't begin to translate.

Through the haze of pain that fogged her mind, it all meant nothing to Cortana at the time. Her captors, however, felt differently.

R'izaymmir had noticed the human prisoner drop to her knees, and snapped his split mandibles in irritation; humans were so weak and fragile compared to the sheer power of his own race, and he despised having to handle such frail creatures, much less be in the same room with them. He stalked over to the fallen prisoner, swiftly kicking out at her with a cold indifference.

"On your feet, human!" he snapped, reaching down to grab Cortana's shoulder. He lifted her up bodily, one hand clutching her torn shirt, and abruptly let go when her face lifted to meet his.

Instead of the light auburn color her eyes had been the night before, when she had first been brought aboard the Covenant vessel, Cortana's now sightless eyes were a vivid purple color, and pupil-less. Letters and numbers streamed in a meaningless jumble across her eyes, and Cortana continued to make strangled gasps of protest and pain as her thin fingers scrabbled at her face in an attempt to ease the pain.

R'izaymmir abruptly shoved Cortana out of line, and she stumbled towards the other two Elites, oblivious to anything but the throbbing that still sliced through her mind.

"Take her to a solitary confinement medical room," R'izaymmir demanded to one of his companions. "Do what you will to the others, but leave her untouched until I see to her personally."


End file.
